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swolock / scrublet

Detect doublets in single-cell RNA-seq data
MIT License
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Illegal instruction core dumped error #50

Open PDhingra2016 opened 1 year ago

PDhingra2016 commented 1 year ago

HI I have recently started using scrublet. Thanks for making it availabel for scientific community. Scrublet worked fine for me for some of the snRNA-seq samples but recently it started giving me error. Even I am unable to run PBMC example on your github. scrub_doublets code run till Embedding transcriptome using PCA step but gives core dumped at Calculating doublet scores. I am not an expert in python but tried increased RAM and ulimit based on google serch for core dumped error. Nothing helped.

Your help will be greatly appreciated Thanks Priyanka

doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2,
...                                                           min_cells=3,
...                                                           min_gene_variability_pctl=85,
...                                                           n_prin_comps=30)
Preprocessing...
Simulating doublets...
Embedding transcriptomes using PCA...
Calculating doublet scores...
Illegal instruction (core dumped)
karlacat1 commented 1 year ago

Are there any updates on this? I have the same error. Thanks!

fthommen commented 1 year ago

@PDhingra2016 this problem is most surely not a problem of scrublet but of the used Annoy library. See e.g. https://github.com/spotify/annoy/issues/506, https://github.com/spotify/annoy/issues/513 and https://github.com/openpipelines-bio/openpipeline/issues/265. I had to back as far as annoy 1.15.2 to run the example code w/o crash on certain hardware platforms. YMMV

@karlacat1 I've already answered you inhouse 😄